Most state taxes can't be completed until the federal 1040 is done. / Thinkstock

by Kevin McCoy, USA TODAY

by Kevin McCoy, USA TODAY

It's beginning to look a lot like a particularly miserable federal tax-filing season.

Millions of U.S. taxpayers could become subject to the federal alternative minimum tax and face delays in filing their tax returns - and collecting refunds - unless Washington leaders resolve their down-to-the-wire fiscal cliff impasse.

Enacted in 1969, the alternative minimum tax was originally intended to ensure that the nation's wealthiest taxpayers paid at least some income tax. The levy takes effect at a specific income level, and isn't indexed to account for inflation.

Instead, the Internal Revenue Service counts on Congress to enact an annual "patch" that spares millions of additional lower-income earners from higher levies under the alternative minimum tax. But this year's fiscal cliff standoff has so far left the higher tax threat unpatched.

"This means that, absent enactment of a new patch in the near future, nearly 30 million additional taxpayers will become subject to the AMT on their 2012 income tax returns," Acting IRS Commissioner Steven Miller wrote last week to Rep. Sander Levin, D-Mich., the ranking minority member of the House Ways and Means Committee.

Significantly, the 2012 exemption ceilings for the alternative minimum tax "are much lower," wrote Miller: $45,000 for joint filers and $33,750 for single taxpayers.

Absent a fiscal cliff deal by year's end, which remains possible, the IRS would have to reprogram its computers to account for lack of action on the alternative minimum tax. The complexity and scope of the changes necessary could leave the IRS unable to accept tax returns well into 2013.

"Most taxpayers may not be able to file their 2012 tax returns until late in March of 2013, or even later," warned Miller, who estimated that as many as 100 million of the projected 150 million total federal tax returns could be affected.

Such a delay would mean similarly late refunds for many filers. The IRS issued nearly 119.9 million refunds during fiscal year 2011 for individual income tax returns, the tax agency's data show.

"Since Congress is still considering changes to the tax law, we continue to closely monitor the situation. We intend to issue guidance by the end of the year on appropriate withholding for 2013," the IRS said in a statement just before the agency closed for the Christmas holiday.

Employers are anxiously waiting for definitive news, Brian O'Laughlin, manager of government relations for the American Payroll Association, said hours before Christmas Eve. But for many large payroll processors, the first January 2013 paychecks have already been completed using 2012 withholding rates.

If those rates change, as is widely anticipated in any fiscal-cliff agreement, employers could have to withhold more taxes later in January or further into 2013 to cover any shortfall and spare employees from larger tax bills or penalties when the workers file 2013 federal tax returns.